esetSpectralMap {esetVis} | R Documentation

## plot a spectral map biplot of an eSet.

### Description

`esetSpectralMap` reduces the dimension of the data contained in the eSet with the `mpm` function and plot the subsequent biplot of the specified dimensions, possibly with gene and sample annotation contained in the eSet. A spectral map with the default parameters is equivalent to a principal component analysis on the log-transformed, double centered and global normalized data (from documentation of the `mpm` function).

### Usage

    esetSpectralMap(eset, psids = 1:nrow(eset), dim = c(1, 2),
      colorVar = character(), color = if (length(colorVar) == 0) "black"
      else character(), shapeVar = character(), shape = if
      (length(shapeVar) == 0) 15 else numeric(), sizeVar = character(),
      size = if (length(sizeVar) == 0) {     ifelse(typePlot == "interactive"
      && length(packageInteractivity) == 1 && packageInteractivity == "rbokeh",
      5, 2.5) } else {     numeric() }, sizeRange = numeric(),
      alphaVar = character(), alpha = if (length(alphaVar) == 0) 1 else
      numeric(), alphaRange = numeric(), title = "",
      mpm.args = list(closure = "none", center = "double", normal = "global",
      row.weight = "mean", col.weight = "constant", logtrans = FALSE),
      plot.mpm.args = list(scale = "uvc"), symmetryAxes = c("combine",
      "separate", "none"), packageTextLabel = c("ggrepel", "ggplot2"),
      cloudGenes = TRUE, cloudGenesColor = "black",
      cloudGenesNBins = sqrt(length(psids)),
      cloudGenesIncludeLegend = FALSE, cloudGenesTitleLegend = "nGenes",
      topGenes = 10, topGenesCex = 2.5, topGenesVar = character(),
      topGenesJust = c(0.5, 0.5), topGenesColor = "black",
      topSamples = 10, topSamplesCex = 2.5, topSamplesVar = character(),
      topSamplesJust = c(0.5, 0.5), topSamplesColor = "black",
      geneSets = list(), geneSetsVar = character(),
      geneSetsMaxNChar = numeric(), topGeneSets = 10,
      topGeneSetsCex = 2.5, topGeneSetsJust = c(0.5, 0.5),
      topGeneSetsColor = "black", includeLegend = TRUE,
      includeLineOrigin = TRUE, typePlot = c("static", "interactive"),
      packageInteractivity = c("rbokeh", "ggvis"),
      figInteractiveSize = c(600, 400), ggvisAdjustLegend = TRUE,
      interactiveTooltip = TRUE, interactiveTooltipExtraVars = character(),
      returnAnalysis = FALSE, returnEsetPlot = FALSE)

### Arguments

`eset` | expressionSet (or SummarizedExperiment) object with data
`psids` | featureNames of genes to include in the plot, all by default
`dim` | dimensions of the analysis to represent, first two dimensions by default
`colorVar` | name of variable (in varLabels of the `eset`) used for coloring, empty by default
`color` | character or factor with specified color(s) for the points, replicated if needed. This is used only if `colorVar` is empty. By default: 'black' if `colorVar` is not specified and default `ggplot` palette otherwise
`shapeVar` | name of variable (in varLabels of the `eset`) used for the shape, empty by default
`shape` | character or factor with specified shape(s) (pch) for the points, replicated if needed. This is used only if `shapeVar` is empty. By default: '15' (filled square) if `shapeVar` is not specified and default `ggplot` shape(s) otherwise
`sizeVar` | name of variable (in varLabels of the `eset`) used for the size, empty by default
`size` | character or factor with specified size(s) (cex) for the points, replicated if needed. This is used only if `sizeVar` is empty. By default: '2.5' if `sizeVar` is not specified and default `ggplot` size(s) otherwise
`sizeRange` | size (cex) range used in the plot, possible only if the `sizeVar` is 'numeric' or 'integer'
`alphaVar` | name of variable (in varLabels of the `eset`) used for the transparency, empty by default. This parameter is currently only available for static plot and ggvis (only numeric in this case).
`alpha` | character or factor with specified transparency(s) for the points, replicated if needed. This is used only if `shapeVar` is empty. By default: '1' if `alphaVar` is not specified and default `ggplot` alpha otherwise This parameter is currently only available for static and ggvis.
`alphaRange` | transparency (alpha) range used in the plot, possible only if the `alphaVar` is 'numeric' or 'integer' This parameter is currently only available for static and ggvis plot.
`title` | plot title, ” by default
`mpm.args` | list with input parameters for the `mpm` function. The default value is: `list(closure = 'none', center = 'double', normal = 'global', 'row.weight' = 'mean', col.weight = 'constant', logtrans = FALSE)`. This assumes that the data are already in a log scale.
`plot.mpm.args` | list with input parameters for the `plot.mpm` function. The default value is: list(scale = "uvc").
`symmetryAxes` | set symmetry for axes, either: 'combine' (by default): both axes are symmetric and with the same limits 'separate': each axis is symmetric and has its own limits 'none': axes by default (plot limits)
`packageTextLabel` | package used to label the outlying genes/samples/gene sets, either `ggrepel` (by default, only used if package `ggrepel` is available), or `ggplot2`
`cloudGenes` | logical, if TRUE (by default), include the cloud of genes in the plot
`cloudGenesColor` | if `cloudGenes` is TRUE, color for the cloud of genes, black by default
`cloudGenesNBins` | number of bins to used for the clouds of genes, by default the square root of the number of genes
`cloudGenesIncludeLegend` | logical, if TRUE (FALSE by default) include the legend for the cloud of genes (in the top position if multiple legends)
`cloudGenesTitleLegend` | string with title for the legend for the cloud of genes 'nGenes' by default
`topGenes` | numeric indicating which percentile (if <1) or number (if >=1) of genes most distant to the origin of the plot to annotate, by default: 10 genes are selected If no genes should be annotated, set this parameter to 0 Currently only available for static plot.
`topGenesCex` | cex for gene annotation (used when `topGenes` > 0)
`topGenesVar` | variable of the featureData used to label the genes, by default: empty, the featureNames are used for labelling (used when `topGenes` > 0)
`topGenesJust` | text justification for the genes (used when `topGenes` > 0 and if `packageTextLabel` is `ggplot2`), by default: c(0.5, 0.5) so centered
`topGenesColor` | text color for the genes (used when `topGenes` > 0), black by default
`topSamples` | numeric indicating which percentile (if <1) or number (if >=1) of samples most distant to the origin of the plot to annotate, by default: 10 samples are selected If no samples should be annotated, set this parameter to 0. Currently available for static plot.
`topSamplesCex` | cex for sample annotation (used when `topSamples` > 0)
`topSamplesVar` | variable of the phenoData used to label the samples, by default: empty, the sampleNames are used for labelling (used when `topSample`s > 0)
`topSamplesJust` | text justification for the samples (used when `topSamples` > 0 and if `packageTextLabel` is `ggplot2`), by default: c(0.5, 0.5) so centered
`topSamplesColor` | text color for the samples (used when `topSamples` > 0), black by default
`geneSets` | list of gene sets/pathways, each containing identifiers of genes contained in the set. E.g. pathways from Gene Ontology databases output from the `getGeneSetsForPlot` function or any custom list of pathways. The genes identifiers should correspond to the variable `geneSetsVar` contained in the phenoData, if not specified the featureNames are used. If several gene sets have the same name, they will be combine to extract the top gene sets.
`geneSetsVar` | variable of the featureData used to match the genes contained in geneSets, most probably ENTREZID, if not specified the featureNames of the eSet are used Only used when `topGeneSets` > 0 and the parameter geneSets is specified.
`geneSetsMaxNChar` | maximum number of characters for pathway names, by default keep entire names Only used when `topGeneSets` > 0 and the parameter `geneSets` is specified. If `returnAnalysis` is set to TRUE and `geneSetsMaxNChar` specified, the top pathways will be returned in the output object, named with the identifiers used in the plot (so with maximum `geneSetsMaxNChar` number of characters)
`topGeneSets` | numeric indicating which percentile (if <=1) or number (if >1) of gene sets most distant to the origin of the plot to annotate, by default: 10 gene sets are selected If no gene sets should be annotated, set this parameter to 0. Currently available for static plot. Only used when `topGeneSets` > 0 and the parameter geneSets is specified.
`topGeneSetsCex` | cex for gene sets annotation Only used when `topGeneSets` > 0 and the parameter geneSets is specified.
`topGeneSetsJust` | text justification for the gene sets by default: c(0.5, 0.5) so centered Only used when `topGeneSets` > 0, the parameter `geneSets` is specified and if `packageTextLabel` is `ggplot2`.
`topGeneSetsColor` | color for the gene sets (used when `topGeneSets` > 0 and `geneSets` is specified), black by default Only used when `topGeneSets` > 0 and the parameter geneSets is specified.
`includeLegend` | logical if TRUE (by default) include a legend, otherwise not
`includeLineOrigin` | if TRUE (by default) include vertical line at x = 0 and horizontal line at y = 0
`typePlot` | type of the plot returned, either 'static' (static) or interactive' (potentially interactive)
`packageInteractivity` | if `typePlot` is 'interactive', package used for interactive plot, either 'rbokeh' (by default) or 'ggvis'
`figInteractiveSize` | vector containing the size of the interactive plot, as [width, height] by default: c(600, 400). This is passed to the `width` and `height` parameters of: for rbokeh plots: the `bokeh::figure` function for ggvis plots: the `ggvis::set_options` function
`ggvisAdjustLegend` | logical, if TRUE (by default) adjust the legends in `ggvis` to avoid overlapping legends when multiple legends
`interactiveTooltip` | logical, if TRUE, add hoover functionality showing sample annotation (variables used in the plot) in the plot
`interactiveTooltipExtraVars` | name of extra variable(s) (in varLabels of the `eset`) to add in rbokehEsetPlot to label the samples, empty by default
`returnAnalysis` | logical, if TRUE (FALSE by default), return also the output of the analysis, and the outlying samples in the topElements element if any, otherwise only the plot object
`returnEsetPlot` | logical, if TRUE return also the esetPlot object

### Value

if `returnAnalysis` is TRUE, return a list:

- analysis: output of the spectral map analysis, can be given as input to the `esetPlotWrapper` function

  - dataPlotSamples: coordinates of the samples

  - dataPlotGenes: coordinates of the genes

  - esetUsed: expressionSet used in the plot

  - axisLabels: axes labels indicating percentage of variance explained by the selected axes

  - axesContributionsPercentages: percentages of variance explained by each axis (not only the ones specified in `dim`)

- topElements: list with top outlying elements if any, possibly genes, samples and gene sets

- plot: the plot output

otherwise return only the plot

### Author(s)

Laure Cougnaud

### References

Lewi, P.J. (1976). Spectral mapping, a technique for classifying biological activity profiles of chemical compounds. Arzneimittel Forschung (Drug Research), 26, 1295–1300

### See Also

the function used internally: `mpm` and `spectralMap` for spectral map in base R graphics

### Examples

    library(ALL)
    data(ALL)

    ## complete example (most of the parameters are optional)
    # create custom color palette
    colorPalette <- c("dodgerblue", colorRampPalette(c("white","dodgerblue2", "darkblue"))(5)[-1],
    	"red", colorRampPalette(c("white", "red3", "darkred"))(5)[-1])
    # plot the spectral map
    print(esetSpectralMap(eset = ALL,
    	title = "Acute lymphoblastic leukemia dataset \n Spectral map complete",
    colorVar = "BT", color = colorPalette,
    shapeVar = "sex", shape = 15:16,
    sizeVar = "age", sizeRange = c(2, 6),
    symmetryAxes = "separate",
    topGenes = 10, topGenesJust = c(1, 0), topGenesCex = 2, topGenesColor = "darkgrey",
    topSamples = 15, topSamplesVar = "cod", topSamplesColor = "black",
    topSamplesJust = c(1, 0), topSamplesCex = 3)
    )

    # see vignette for other examples, especially one with gene sets specification

[Package esetVis version 1.12.0 Index]